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-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Keitaro Yamashita
Sent: Monday, April 16, 2012 7:09 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] bulk solvent treatment inside protein cavities
Dear Garib,
Is there REFMAC option to output solvent mask information (e.g. Fmask and
PHImask in mtz to check with Coot)?
I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
But I'm not sure that FC_ALL = FC + FMASK is correct or not.
Keitaro
2012/4/16 Garib N Murshudov <[log in to unmask]>:
> Dear Allister
>
> Could you please update refmac version. In the version you it seems
> that bulk solvent mask calculation has some problems. New version (at
> the moment) can be downloaded from this site:
>
> http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_l
> inux.tar.gz
>
> There is a mac version also.
>
>
> regards
> Garib
>
>
> On 16 Apr 2012, at 11:37, Allister Crow wrote:
>
>
> Board members,
>
> I have a couple of questions regarding how to improve the solvent
> model as applied to solvent-filled cavities inside proteins.
>
> I am currently nearing the end of refinement of a protein structure at
> 2.8 A resolution. I recently switched Refmac versions, upon doing
> this I noticed a modest improvement in R factors, but I also notice
> some new features in the difference maps. These features don't show
> up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands'
> of any form. In fact, I suspect that the appearance of these features
> (which are all located in solvent channels within cavities inside the
> protein) are probably due to some difference in how the bulk solvent
contribution has been applied.
>
> I've attached a picture of one such feature showing the difference
> between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3
> sigma- both using the same model and refinement parameters).
>
> My questions are therefore:
>
> 1) has something substantial changed in the bulk solvent treatment
> between Refmac versions 5.5 and 5.6?
>
> 2) How can I go about changing the bulk solvent treatment to better
> account for solvent contribution inside the protein cavities?
>
> Best wishes, and thanks in advance for all your help,
>
> - Allister Crow
>
>
> <bulk_solvent_inside_cavities.png>
>
>
>
> Dr Garib N Murshudov
> Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge
> CB2 0QH UK
> Email: [log in to unmask]
> Web http://www.mrc-lmb.cam.ac.uk
>
>
>
>
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